Extra commands (#554)

* Extra samtools commands
* Added extra bcftools commands

Author: muffato

registry/quay.io/biocontainers/bcftools/container.yaml

@@ -14,7 +14,13 @@ aliases:
   bcftools: /usr/local/bin/bcftools
   bgzip: /usr/local/bin/bgzip
   color-chrs.pl: /usr/local/bin/color-chrs.pl
+  gff2gff.py: /usr/local/bin/gff2gff.py
   guess-ploidy.py: /usr/local/bin/guess-ploidy.py
   htsfile: /usr/local/bin/htsfile
+  libdeflate-gunzip: /usr/local/bin/libdeflate-gunzip
+  libdeflate-gzip: /usr/local/bin/libdeflate-gzip
+  plot-roh.py: /usr/local/bin/plot-roh.py
+  plot-vcfstats: /usr/local/bin/plot-vcfstats
+  run-roh.pl: /usr/local/bin/run-roh.pl
   tabix: /usr/local/bin/tabix
   vcfutils.pl: /usr/local/bin/vcfutils.pl

registry/quay.io/biocontainers/samtools/container.yaml

@@ -12,7 +12,30 @@ tags:
   1.14--hb421002_0: sha256:88632c41eba8b94b7a2a1013f422aecf478a0cb278740bcc3a38058c903d61ad
   1.15--h3843a85_0: sha256:d68e1b5f504dc60eb9f2a02eecbac44a63f144e7d455b3fb1a25323c667ca4c4
 aliases:
+  ace2sam: /usr/local/bin/ace2sam
   bgzip: /usr/local/bin/bgzip
+  blast2sam.pl: /usr/local/bin/blast2sam.pl
+  bowtie2sam.pl: /usr/local/bin/bowtie2sam.pl
+  export2sam.pl: /usr/local/bin/export2sam.pl
+  fasta-sanitize.pl: /usr/local/bin/fasta-sanitize.pl
   htsfile: /usr/local/bin/htsfile
+  interpolate_sam.pl: /usr/local/bin/interpolate_sam.pl
+  libdeflate-gunzip: /usr/local/bin/libdeflate-gunzip
+  libdeflate-gzip: /usr/local/bin/libdeflate-gzip
+  maq2sam-long: /usr/local/bin/maq2sam-long
+  maq2sam-short: /usr/local/bin/maq2sam-short
+  md5fa: /usr/local/bin/md5fa
+  md5sum-lite: /usr/local/bin/md5sum-lite
+  novo2sam.pl: /usr/local/bin/novo2sam.pl
+  plot-ampliconstats: /usr/local/bin/plot-ampliconstats
+  plot-bamstats: /usr/local/bin/plot-bamstats
+  psl2sam.pl: /usr/local/bin/psl2sam.pl
+  sam2vcf.pl: /usr/local/bin/sam2vcf.pl
   samtools: /usr/local/bin/samtools
+  samtools.pl: /usr/local/bin/samtools.pl
+  seq_cache_populate.pl: /usr/local/bin/seq_cache_populate.pl
+  soap2sam.pl: /usr/local/bin/soap2sam.pl
   tabix: /usr/local/bin/tabix
+  wgsim: /usr/local/bin/wgsim
+  wgsim_eval.pl: /usr/local/bin/wgsim_eval.pl
+  zoom2sam.pl: /usr/local/bin/zoom2sam.pl